#ifndef XENKAT_INPUT_PROCESSOR_HPP_INCLUDED
#define XENKAT_INPUT_PROCESSOR_HPP_INCLUDED

#include <fstream>
using std::ifstream;
using std::ios;

#include <string>
using std::string;

#include <utility>
using std::make_pair;
using std::pair;

typedef string Sequence_name;
typedef string Sequence;
typedef pair<Sequence_name, Sequence> Named_sequence;

Named_sequence get_raw_sequence( ifstream & stream );
Named_sequence get_filtered_sequence( ifstream & stream );

#endif // XENKAT_INPUT_PROCESSOR_HPP_INCLUDED
